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Funding Update for Jan 3, 2011

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NSF Microarray Grants Awarded Aug. 1, 2010 — Jan. 1, 2011

Multiscale Genomic Imaging Informatics
Start Date: Aug. 1, 2010
Expires: Nov. 30, 2011
Awarded amount to date: $336,526
Principal investigator: Yu-Ping Wang
Sponsor: Tulane University

This award funds the creation of an imaging database management and analysis system that can integrate multiscale and multimodality structural genomic information with microarray gene expression data. The project team will develop image processing and signal analysis algorithms to extract visual quantitative traits and structural genomic signatures from the results of high-resolution genomic imaging techniques such as fluorescence in situ hybridization imaging and microarray-based comparative genomic hybridization. These quantitative structural signatures will then be correlated with microarray gene expression patterns. Finally, this multiscale structural and functional information will be integrated for improved characterization of biological systems.


New Theory and Methodology for Large-Scale Multiple Testing
Start date:
Aug. 1, 2010
Expires: July 31, 2011
Awarded amount to date: $50,803
Principal investigator: Wenguang Sun
Sponsor: North Carolina State University

This project focuses on new theories, methodologies, and computational algorithms to address challenges in large-scale multiple testing. These include the concept of simultaneously incorporating statistical significance and effect size in multiple testing and a new approach to identifying large non-null effects in heteroscedastic models; the strategy of exploiting spatial dependency and a new approach to testing correlated hypotheses in a hidden Markov random field; the strategy of grouping hypotheses in sets and a new approach to testing the significance of multiple groups of important variables; and the concepts of discovery boundary and effective screening, and a data-driven approach to reducing dimensionality by constructing subsets that are optimal in size and adaptive to unknown sparsity. According to the investigators, the research may have an impact on genome-wide association studies, time-course microarray experiments, disease mapping in environmental studies, climate modeling, and medical imaging studies.


Design and Implementation of Position-Encoded 3D Microarrays
Start date:
Sept. 1, 2010
Expires: Aug. 31, 2014
Awarded amount to date: $1,187,000
Principal investigators: Arye Nehorai and Axel Scherer
Sponsors: Washington University and California Institute of Technology

The investigators aim to build a three-dimensional microarray device with position-controlled microspheres to perform screening of complementary DNAs, RNAs, and protein receptors on a single platform. This new device will be portable, self-contained, and automatic, and applications of the device could include medical screening, drug discovery, and gene sequencing, according to the investigators.


Metabolomics and Genome Wide Association Mapping for the Elucidation of Triterpene Saponin Molecular Biochemistry in Medicago
Start date:
Sept. 1, 2010
Expires: Aug. 31, 2011
Awarded amount to date: $191,703
Principal investigator: Lloyd Sumner
Sponsor: Samuel Roberts Noble Foundation

The goal of this project is to identify genes responsible for triterpene saponin biosynthesis in Medicago truncatula, an experimental model for leguminous crop species. Triterpene saponins are a class of structurally diverse plant natural products with a wide range of demonstrated bioactivities including allelopathic, antifungal, antibacterial, anti-insect, anticancer, anti-nutritive activities. As part of the project, the investigators will conduct metabolome analyses of a large and diverse M. truncatula germplasm collection to identify high and low saponin accumulating lines and to enable genome-wide association mapping between specific loci with saponin content. They will also perform comparative gene expression analyses of high and low saponin accumulating lines to identify putative genes involved in triterpene saponin biosynthesis and regulation. Finally, molecular and biochemical confirmation of select targeted saponin biosynthetic genes will be prioritized based upon obtained evidence.

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Revitalizing Facilities for Research on Life in Extreme Environments
Start date:
Sept. 1, 2010
Expires: Aug. 31, 2012
Awarded amount to date: $1,150,000
Principal investigator: Anna-Louise Reysenbach
Sponsor: Portland State University

This award provides funds to convert 10,745 square feet in Portland State University's Science Building 2 into a Center for Life in Extreme Environments. The renovations will enable CLEE researchers to conduct research on the ecological and physiological effects of extremes in temperature and pH and extremes in nutrient, water, and oxygen availability. The plan will provide central laboratory support space, and will permit relocation of the microarray facility to the new area.


System Support for Generally Programmable Digital Microfluidic Biochip Devices
Start Date:
Sept. 15, 2010
Expires: Aug. 31, 2013
Awarded amount to date: $539,999
Principal investigator: Philip Brisk
Sponsor: University of California at Riverside

The researchers aim to develop a prototype programmable microfluidic laboratory-on-chip that concurrently executes assays in an online fashion. Using the device, the chemist will be able to specify an assay using a text-based language. Assays will then arrive at the device in real time and an operating system running on an attached microcontroller will interpret them. Ultimately, the researchers hope to develop a software simulation infrastructure for the laboratory-on-chip and to build the operating system on top of it.


Reel-to-Reel Assembly of Lab-on-a-Film Diagnostic Tests
Start date:
Jan. 1, 2011
Expires: June 20, 2011
Awarded amount to date: $149,959
Principal investigator: Christopher Cooney
Sponsor: Akonni Biosystems

This small business innovation research phase I project is designed to investigate the feasibility of using materials and films that can be rolled, so as to determine the possibility of manufacturing a lab-on-a-film microarray device, and to develop a valveless PCR-microarray device in a lab-on-a-film format such that a PCR amplicon is confined to the device. The first objective requires printing microarrays with Akonni's gel drop technology on chemically unmodified thin films with low autofluorescence, and identifying tapes and films that can be rolled to create the lab-on-a-film assembly. The second objective of designing a valveless lab-on-a-film device also is important to transfer the design to a reel-to-reel manufacturing process because the steps associated with adding components for a valve are eliminated. At the end of this project the investigators expect to demonstrate feasibility by positively identifying methicillin-resistant Staphylococcus aureus on a PCR-microarray lab-on-a-film device.


Novel Microarray Platforms for Detection of Rare Molecules in Complex Mixtures
Start Date:
Jan. 1, 2011
Expires: June 30, 2011
Awarded amount to date: $149,499
Principal investigator: Michael Harvey
Sponsor: Maine Manufacturing

This small business innovation research phase I project proposes to construct a new microarray platform with high protein-binding capacity that allows for enhanced fluorescence detection. The investigators aim to construct a composite or modified surface by casting nitrocellulose on an optically transparent porous track-etched membrane, and by directly modifying the track-etched membrane with functional silanes to provide chemical groups permitting covalent coupling of proteins and nucleic acids. This type of modified, optically transparent track-etched membrane may be optimal for antibody arrays where the capture molecule can be immobilized at a sufficient density to provide a sensitive assay surface, according to the project abstract.

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